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Table 1 Oligonucleotides used for PCR amplification of viral and transgene sequences

From: Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues

Primer

Sequence (5'-3')

Target sequence

EAB555/F

(5'-TACATCGGCCTTTGAGTCGCATGG-3')

EACMV DNA B

EAB555/R

(5'-CTTATTAACGCCTATATAAACACC-3')

EACMV DNA B

JSP001

(5'-ATGTCGAAGCGACCAGGAGAT-3')

ACMV (AV1/CP)

JSP002

(5'-TGTTTATTAATTGCCAATACT-3')

ACMV (AV1/CP)

UniF

(5'-KSGGGTCGACGTCATCAATGACGTTRTAC-3')

CMGs DNA A

UniR

(5'-AARGAATTCATKGGGGCCCARARRGACTGGC-3')

CMGs DNA A

MSVF

(5'-ATCCCTCCAAATTCCGACAC-3')

MSV

MSVR

(5'-TCCATGTACAAAGCTCCTCT-3')

MSV

C1F

(5'-GCAGATCTATGCCTCGTTTATTTAAAATATATGC-3')

TYLCV

C1R

(5'-GCGGTACCTTACGCCTTATTGGTTTCTTCTTGGC-3')

TYLCV

TMVF

(5'-GCGGTGGCGGCCGATCCATGGAACTTACAG-3')

TMV

TMVR

(5'-GATTCGAACCCCTCGCTTTAT-3')

TMV

POT1

(5'-gacgaattcTGYGAYGCBGATGGYTC-3')

TEV & PVY

POT2

(3'-ACCACRTADCTBTTAcctaggtcag-5')

TEV & PVY

AC1F

(5'-ATGAGAACTCCTCGTTTTAGAA-3')

ACMV-Kenya AC1

AC1R

(5'-ATGAGAACTCCT CGTTTTAGAA-3')

ACMV-Kenya AC1

MP141

(5'-ATGATTGAACAAGATGGATTGCAC-3')

Npt II coding sequence

MP142

(5'-TCAGAAGAACTCGTCAAGAAGGCG-3')

Npt II coding sequence

  1. EACMV – East African cassava mosaic virus; ACMV – African cassava mosaic virus; MSV – maize streak virus; TYLCV – tomato yellow leaf curl virus; TMV – tobacco mosaic virus; TEV – tobacco etch virus; PVY – potato virus Y
  2. EAB555/F &EAB555/R: PCR conditions consisted of 30 cycles of 94°C for 1 min, 58°C for 1 min. and 72°C for 2 mins.
  3. JSP001 &JSP002: PCR conditions consisted of 30 cycles of 94°C for 1 min, 45°C for 1 min. and 72°C for 2 mins.
  4. Uni F &Uni R: K = G + T, R = A + G, S = G + C. PCR conditions consisted of 30 cycles of 94°C for 1 min., 58°C for 1 min. and 72°C for 2 min.
  5. MSV F &MSVR : PCR conditions consisted of 30 cycles of 94°C for 1 min, 59°C for 1 min and 72°C for 2 mins.
  6. C1F &C2R: PCR conditions consisted of 94°C for 10 mins followed by 35 cycles of 94°C for 30 secs., 60°C for 1 min and 72°C for 1.5 mins followed and extension of 7 mins at 72°C.
  7. AC1F &AC1R : PCR conditions consisted 94°C of 5 mins followed by 35 cycles of 94°C for 30 secs, 58°C for 1 min. and 72°C for 1 mins followed by extension of 10 mins at 72°C.
  8. MP141 &MP142: PCR conditions consisted 5 mins. at 94°C followed by 35 cycles of 94°C for 30 secs, 58°C for 1 min. and 72°C for 1 mins. followed by extension time of 10 mins. at 72°C.
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Virology Journal

ISSN: 1743-422X